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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 690 by mmeineke, Tue Aug 12 21:44:06 2003 UTC vs.
Revision 962 by tim, Mon Jan 19 18:36:21 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8		#include "ReadWrite.hpp"
9		#include "parse_me.h"
#	Line 21 | Line 21
21		#define NVT_ENS        1
22		#define NPTi_ENS       2
23		#define NPTf_ENS       3
24	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
24	>	#define NPTxyz_ENS     4
25
26	+
27		#define FF_DUFF 0
28		#define FF_LJ   1
29		#define FF_EAM  2
30
31		using namespace std;
32
33	+	/**
34	+	* Check whether dividend is divisble by divisor or not
35	+	*/
36	+	bool isDivisible(double dividend, double divisor){
37	+	double tolerance = 0.000001;
38	+	double quotient;
39	+	double diff;
40	+	int intQuotient;
41	+
42	+	quotient = dividend / divisor;
43	+
44	+	if (quotient < 0)
45	+	quotient = -quotient;
46	+
47	+	intQuotient = int (quotient + tolerance);
48	+
49	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50	+
51	+	if (diff <= tolerance)
52	+	return true;
53	+	else
54	+	return false;
55	+	}
56	+
57		SimSetup::SimSetup(){
58
59	+	initSuspend = false;
60		isInfoArray = 0;
61		nInfo = 1;
62	<
62	>
63		stamps = new MakeStamps();
64		globals = new Globals();
65	<
66	<
65	>
66	>
67		#ifdef IS_MPI
68	<	strcpy( checkPointMsg, "SimSetup creation successful" );
68	>	strcpy(checkPointMsg, "SimSetup creation successful");
69		MPIcheckPoint();
70		#endif // IS_MPI
71		}
#	Line 50 | Line 75 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
75		delete globals;
76		}
77
78	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
79	<	info = the_info;
80	<	nInfo = theNinfo;
81	<	isInfoArray = 1;
78	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
79	>	info = the_info;
80	>	nInfo = theNinfo;
81	>	isInfoArray = 1;
82	>	initSuspend = true;
83		}
84
85
86	<	void SimSetup::parseFile( char* fileName ){
61	<
86	>	void SimSetup::parseFile(char* fileName){
87		#ifdef IS_MPI
88	<	if( worldRank == 0 ){
88	>	if (worldRank == 0){
89		#endif // is_mpi
90	<
90	>
91		inFileName = fileName;
92	<	set_interface_stamps( stamps, globals );
93	<
92	>	set_interface_stamps(stamps, globals);
93	>
94		#ifdef IS_MPI
95		mpiEventInit();
96		#endif
97
98	<	yacc_BASS( fileName );
98	>	yacc_BASS(fileName);
99
100		#ifdef IS_MPI
101		throwMPIEvent(NULL);
102		}
103	<	else receiveParse();
103	>	else{
104	>	receiveParse();
105	>	}
106		#endif
107
108		}
109
110		#ifdef IS_MPI
111		void SimSetup::receiveParse(void){
112	<
113	<	set_interface_stamps( stamps, globals );
114	<	mpiEventInit();
115	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
112	>	set_interface_stamps(stamps, globals);
113	>	mpiEventInit();
114	>	MPIcheckPoint();
115	>	mpiEventLoop();
116		}
117
118		#endif // is_mpi
119
120		void SimSetup::createSim(void){
121
97	–	int i, j, k, globalAtomIndex;
98	–
122		// gather all of the information from the Bass file
123
124		gatherInfo();
#	Line 110 | Line 133 | void SimSetup::createSim(void){
133
134		// initialize the system coordinates
135
136	<	if( !isInfoArray ) initSystemCoords();
136	>	if ( !initSuspend ){
137	>	initSystemCoords();
138
139	+	if( !(globals->getUseInitTime()) )
140	+	info[0].currentTime = 0.0;
141	+	}
142	+
143		// make the output filenames
144
145		makeOutNames();
146	<
146	>
147		// make the integrator
148	<
148	>
149		makeIntegrator();
150	<
150	>
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 127 | Line 155 | void SimSetup::createSim(void){
155		// initialize the Fortran
156
157		initFortran();
130	–
131	–
132	–
158		}
159
160
161	<	void SimSetup::makeMolecules( void ){
162	<
138	<	int k,l;
161	>	void SimSetup::makeMolecules(void){
162	>	int k;
163		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164		molInit molInfo;
165		DirectionalAtom* dAtom;
#	Line 150 | Line 174 | void SimSetup::makeMolecules( void ){
174		bend_set* theBends;
175		torsion_set* theTorsions;
176
177	<
177	>
178		//init the forceField paramters
179
180		the_ff->readParams();
181
182	<
182	>
183		// init the atoms
184
185		double ux, uy, uz, u, uSqr;
162	–
163	–	for(k=0; k<nInfo; k++){
164	–
165	–	the_ff->setSimInfo( &(info[k]) );
186
187	+	for (k = 0; k < nInfo; k++){
188	+	the_ff->setSimInfo(&(info[k]));
189	+
190		atomOffset = 0;
191		excludeOffset = 0;
192	<	for(i=0; i<info[k].n_mol; i++){
170	<
192	>	for (i = 0; i < info[k].n_mol; i++){
193		stampID = info[k].molecules[i].getStampID();
194
195	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
196	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
197	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
195	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
196	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
197	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
198		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
199		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
200	<
200	>
201		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
202		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
203	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
204	<	molInfo.myBends = new Bend*[molInfo.nBends];
205	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
203	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
204	>	molInfo.myBends = new Bend * [molInfo.nBends];
205	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
206
207		theBonds = new bond_pair[molInfo.nBonds];
208		theBends = new bend_set[molInfo.nBends];
209		theTorsions = new torsion_set[molInfo.nTorsions];
210	<
210	>
211		// make the Atoms
212	<
213	<	for(j=0; j<molInfo.nAtoms; j++){
214	<
215	<	currentAtom = comp_stamps[stampID]->getAtom( j );
216	<	if( currentAtom->haveOrientation() ){
217	<
218	<	dAtom = new DirectionalAtom( (j + atomOffset),
219	<	info[k].getConfiguration() );
220	<	info[k].n_oriented++;
221	<	molInfo.myAtoms[j] = dAtom;
222	<
223	<	ux = currentAtom->getOrntX();
224	<	uy = currentAtom->getOrntY();
225	<	uz = currentAtom->getOrntZ();
226	<
227	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
228	<
229	<	u = sqrt( uSqr );
230	<	ux = ux / u;
231	<	uy = uy / u;
232	<	uz = uz / u;
233	<
234	<	dAtom->setSUx( ux );
235	<	dAtom->setSUy( uy );
236	<	dAtom->setSUz( uz );
237	<	}
238	<	else{
239	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
240	<	info[k].getConfiguration() );
241	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
212	>
213	>	for (j = 0; j < molInfo.nAtoms; j++){
214	>	currentAtom = comp_stamps[stampID]->getAtom(j);
215	>	if (currentAtom->haveOrientation()){
216	>	dAtom = new DirectionalAtom((j + atomOffset),
217	>	info[k].getConfiguration());
218	>	info[k].n_oriented++;
219	>	molInfo.myAtoms[j] = dAtom;
220	>
221	>	ux = currentAtom->getOrntX();
222	>	uy = currentAtom->getOrntY();
223	>	uz = currentAtom->getOrntZ();
224	>
225	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
226	>
227	>	u = sqrt(uSqr);
228	>	ux = ux / u;
229	>	uy = uy / u;
230	>	uz = uz / u;
231	>
232	>	dAtom->setSUx(ux);
233	>	dAtom->setSUy(uy);
234	>	dAtom->setSUz(uz);
235	>	}
236	>	else{
237	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
238	>	info[k].getConfiguration());
239	>	}
240	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
241	>
242		#ifdef IS_MPI
243	<
244	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
245	<
243	>
244	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
245	>
246		#endif // is_mpi
247		}
248	<
249	<	// make the bonds
250	<	for(j=0; j<molInfo.nBonds; j++){
251	<
252	<	currentBond = comp_stamps[stampID]->getBond( j );
253	<	theBonds[j].a = currentBond->getA() + atomOffset;
254	<	theBonds[j].b = currentBond->getB() + atomOffset;
255	<
256	<	exI = theBonds[j].a;
257	<	exJ = theBonds[j].b;
258	<
259	<	// exclude_I must always be the smaller of the pair
260	<	if( exI > exJ ){
261	<	tempEx = exI;
262	<	exI = exJ;
263	<	exJ = tempEx;
244	<	}
248	>
249	>	// make the bonds
250	>	for (j = 0; j < molInfo.nBonds; j++){
251	>	currentBond = comp_stamps[stampID]->getBond(j);
252	>	theBonds[j].a = currentBond->getA() + atomOffset;
253	>	theBonds[j].b = currentBond->getB() + atomOffset;
254	>
255	>	exI = theBonds[j].a;
256	>	exJ = theBonds[j].b;
257	>
258	>	// exclude_I must always be the smaller of the pair
259	>	if (exI > exJ){
260	>	tempEx = exI;
261	>	exI = exJ;
262	>	exJ = tempEx;
263	>	}
264		#ifdef IS_MPI
265	<	tempEx = exI;
266	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
267	<	tempEx = exJ;
268	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
269	<
270	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
265	>	tempEx = exI;
266	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
267	>	tempEx = exJ;
268	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
269	>
270	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
271		#else  // isn't MPI
272	<
273	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
272	>
273	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
274		#endif  //is_mpi
275		}
276		excludeOffset += molInfo.nBonds;
277	<
277	>
278		//make the bends
279	<	for(j=0; j<molInfo.nBends; j++){
280	<
281	<	currentBend = comp_stamps[stampID]->getBend( j );
282	<	theBends[j].a = currentBend->getA() + atomOffset;
283	<	theBends[j].b = currentBend->getB() + atomOffset;
284	<	theBends[j].c = currentBend->getC() + atomOffset;
285	<
286	<	if( currentBend->haveExtras() ){
287	<
288	<	extras = currentBend->getExtras();
289	<	current_extra = extras;
290	<
291	<	while( current_extra != NULL ){
292	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
293	<
294	<	switch( current_extra->getType() ){
295	<
296	<	case 0:
297	<	theBends[j].ghost =
298	<	current_extra->getInt() + atomOffset;
299	<	theBends[j].isGhost = 1;
300	<	break;
301	<
302	<	case 1:
303	<	theBends[j].ghost =
304	<	(int)current_extra->getDouble() + atomOffset;
305	<	theBends[j].isGhost = 1;
306	<	break;
307	<
308	<	default:
309	<	sprintf( painCave.errMsg,
310	<	"SimSetup Error: ghostVectorSource was neither a "
311	<	"double nor an int.\n"
312	<	"-->Bend[%d] in %s\n",
313	<	j, comp_stamps[stampID]->getID() );
314	<	painCave.isFatal = 1;
315	<	simError();
316	<	}
317	<	}
318	<
319	<	else{
320	<
321	<	sprintf( painCave.errMsg,
322	<	"SimSetup Error: unhandled bend assignment:\n"
323	<	"    -->%s in Bend[%d] in %s\n",
324	<	current_extra->getlhs(),
325	<	j, comp_stamps[stampID]->getID() );
326	<	painCave.isFatal = 1;
327	<	simError();
328	<	}
329	<
330	<	current_extra = current_extra->getNext();
331	<	}
332	<	}
333	<
334	<	if( !theBends[j].isGhost ){
335	<
336	<	exI = theBends[j].a;
337	<	exJ = theBends[j].c;
338	<	}
339	<	else{
340	<
322	<	exI = theBends[j].a;
323	<	exJ = theBends[j].b;
324	<	}
325	<
326	<	// exclude_I must always be the smaller of the pair
327	<	if( exI > exJ ){
328	<	tempEx = exI;
329	<	exI = exJ;
330	<	exJ = tempEx;
331	<	}
279	>	for (j = 0; j < molInfo.nBends; j++){
280	>	currentBend = comp_stamps[stampID]->getBend(j);
281	>	theBends[j].a = currentBend->getA() + atomOffset;
282	>	theBends[j].b = currentBend->getB() + atomOffset;
283	>	theBends[j].c = currentBend->getC() + atomOffset;
284	>
285	>	if (currentBend->haveExtras()){
286	>	extras = currentBend->getExtras();
287	>	current_extra = extras;
288	>
289	>	while (current_extra != NULL){
290	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
291	>	switch (current_extra->getType()){
292	>	case 0:
293	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296	>
297	>	case 1:
298	>	theBends[j].ghost = (int) current_extra->getDouble() +
299	>	atomOffset;
300	>	theBends[j].isGhost = 1;
301	>	break;
302	>
303	>	default:
304	>	sprintf(painCave.errMsg,
305	>	"SimSetup Error: ghostVectorSource was neither a "
306	>	"double nor an int.\n"
307	>	"-->Bend[%d] in %s\n",
308	>	j, comp_stamps[stampID]->getID());
309	>	painCave.isFatal = 1;
310	>	simError();
311	>	}
312	>	}
313	>	else{
314	>	sprintf(painCave.errMsg,
315	>	"SimSetup Error: unhandled bend assignment:\n"
316	>	"    -->%s in Bend[%d] in %s\n",
317	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
318	>	painCave.isFatal = 1;
319	>	simError();
320	>	}
321	>
322	>	current_extra = current_extra->getNext();
323	>	}
324	>	}
325	>
326	>	if (!theBends[j].isGhost){
327	>	exI = theBends[j].a;
328	>	exJ = theBends[j].c;
329	>	}
330	>	else{
331	>	exI = theBends[j].a;
332	>	exJ = theBends[j].b;
333	>	}
334	>
335	>	// exclude_I must always be the smaller of the pair
336	>	if (exI > exJ){
337	>	tempEx = exI;
338	>	exI = exJ;
339	>	exJ = tempEx;
340	>	}
341		#ifdef IS_MPI
342	<	tempEx = exI;
343	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344	<	tempEx = exJ;
345	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346	<
347	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
342	>	tempEx = exI;
343	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344	>	tempEx = exJ;
345	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346	>
347	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
348		#else  // isn't MPI
349	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
350		#endif  //is_mpi
351		}
352		excludeOffset += molInfo.nBends;
353	<
354	<	for(j=0; j<molInfo.nTorsions; j++){
355	<
356	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
357	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
358	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
359	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
360	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
361	<
362	<	exI = theTorsions[j].a;
363	<	exJ = theTorsions[j].d;
364	<
365	<	// exclude_I must always be the smaller of the pair
366	<	if( exI > exJ ){
367	<	tempEx = exI;
368	<	exI = exJ;
369	<	exJ = tempEx;
361	<	}
353	>
354	>	for (j = 0; j < molInfo.nTorsions; j++){
355	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360	>
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363	>
364	>	// exclude_I must always be the smaller of the pair
365	>	if (exI > exJ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370		#ifdef IS_MPI
371	<	tempEx = exI;
372	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	<	tempEx = exJ;
374	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	<
376	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>
376	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
377		#else  // isn't MPI
378	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
378	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
379		#endif  //is_mpi
380		}
381		excludeOffset += molInfo.nTorsions;
382	<
383	<
382	>
383	>
384		// send the arrays off to the forceField for init.
377	–
378	–	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	–	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	–	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	–	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	–
383	–
384	–	info[k].molecules[i].initialize( molInfo );
385
386	<
386	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
387	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
388	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
389	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
390	>	theTorsions);
391	>
392	>
393	>	info[k].molecules[i].initialize(molInfo);
394	>
395	>
396		atomOffset += molInfo.nAtoms;
397		delete[] theBonds;
398		delete[] theBends;
399		delete[] theTorsions;
400		}
401		}
402	<
402	>
403		#ifdef IS_MPI
404	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
404	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
405		MPIcheckPoint();
406		#endif // is_mpi
407	<
407	>
408		// clean up the forcefield
409
410		the_ff->calcRcut();
411		the_ff->cleanMe();
403	–
412		}
413
414	<	void SimSetup::initFromBass( void ){
407	<
414	>	void SimSetup::initFromBass(void){
415		int i, j, k;
416		int n_cells;
417		double cellx, celly, cellz;
#	Line 418 | Line 425 | void SimSetup::initFromBass( void ){
425		vel[1] = 0.0;
426		vel[2] = 0.0;
427
428	<	temp1 = (double)tot_nmol / 4.0;
429	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
430	<	temp3 = ceil( temp2 );
428	>	temp1 = (double) tot_nmol / 4.0;
429	>	temp2 = pow(temp1, (1.0 / 3.0));
430	>	temp3 = ceil(temp2);
431
432	<	have_extra =0;
433	<	if( temp2 < temp3 ){ // we have a non-complete lattice
434	<	have_extra =1;
432	>	have_extra = 0;
433	>	if (temp2 < temp3){
434	>	// we have a non-complete lattice
435	>	have_extra = 1;
436
437	<	n_cells = (int)temp3 - 1;
437	>	n_cells = (int) temp3 - 1;
438		cellx = info[0].boxL[0] / temp3;
439		celly = info[0].boxL[1] / temp3;
440		cellz = info[0].boxL[2] / temp3;
441	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
442	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
443	<	n_per_extra = (int)ceil( temp1 );
441	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
442	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
443	>	n_per_extra = (int) ceil(temp1);
444
445	<	if( n_per_extra > 4){
446	<	sprintf( painCave.errMsg,
447	<	"SimSetup error. There has been an error in constructing"
448	<	" the non-complete lattice.\n" );
445	>	if (n_per_extra > 4){
446	>	sprintf(painCave.errMsg,
447	>	"SimSetup error. There has been an error in constructing"
448	>	" the non-complete lattice.\n");
449		painCave.isFatal = 1;
450		simError();
451		}
452		}
453		else{
454	<	n_cells = (int)temp3;
454	>	n_cells = (int) temp3;
455		cellx = info[0].boxL[0] / temp3;
456		celly = info[0].boxL[1] / temp3;
457		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 462 | void SimSetup::initFromBass( void ){
462		current_comp = 0;
463		current_atom_ndx = 0;
464
465	<	for( i=0; i < n_cells ; i++ ){
466	<	for( j=0; j < n_cells; j++ ){
467	<	for( k=0; k < n_cells; k++ ){
465	>	for (i = 0; i < n_cells ; i++){
466	>	for (j = 0; j < n_cells; j++){
467	>	for (k = 0; k < n_cells; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469
470	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
471
472	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
472	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
473
474	<	makeElement( i * cellx,
470	<	j * celly + 0.5 * celly,
471	<	k * cellz + 0.5 * cellz );
472	<
473	<	makeElement( i * cellx + 0.5 * cellx,
474	<	j * celly,
475	<	k * cellz + 0.5 * cellz );
474	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
475		}
476		}
477		}
478
479	<	if( have_extra ){
479	>	if (have_extra){
480		done = 0;
481
482		int start_ndx;
483	<	for( i=0; i < (n_cells+1) && !done; i++ ){
484	<	for( j=0; j < (n_cells+1) && !done; j++ ){
485	<
486	<	if( i < n_cells ){
483	>	for (i = 0; i < (n_cells + 1) && !done; i++){
484	>	for (j = 0; j < (n_cells + 1) && !done; j++){
485	>	if (i < n_cells){
486	>	if (j < n_cells){
487	>	start_ndx = n_cells;
488	>	}
489	>	else
490	>	start_ndx = 0;
491	>	}
492	>	else
493	>	start_ndx = 0;
494
495	<	if( j < n_cells ){
496	<	start_ndx = n_cells;
497	<	}
492	<	else start_ndx = 0;
493	<	}
494	<	else start_ndx = 0;
495	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
496	>	makeElement(i * cellx, j * celly, k * cellz);
497	>	done = (current_mol >= tot_nmol);
498
499	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
499	>	if (!done && n_per_extra > 1){
500	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
501	>	k * cellz);
502	>	done = (current_mol >= tot_nmol);
503	>	}
504
505	<	makeElement( i * cellx,
506	<	j * celly,
507	<	k * cellz );
508	<	done = ( current_mol >= tot_nmol );
505	>	if (!done && n_per_extra > 2){
506	>	makeElement(i * cellx, j * celly + 0.5 * celly,
507	>	k * cellz + 0.5 * cellz);
508	>	done = (current_mol >= tot_nmol);
509	>	}
510
511	<	if( !done && n_per_extra > 1 ){
512	<	makeElement( i * cellx + 0.5 * cellx,
513	<	j * celly + 0.5 * celly,
514	<	k * cellz );
515	<	done = ( current_mol >= tot_nmol );
516	<	}
509	<
510	<	if( !done && n_per_extra > 2){
511	<	makeElement( i * cellx,
512	<	j * celly + 0.5 * celly,
513	<	k * cellz + 0.5 * cellz );
514	<	done = ( current_mol >= tot_nmol );
515	<	}
516	<
517	<	if( !done && n_per_extra > 3){
518	<	makeElement( i * cellx + 0.5 * cellx,
519	<	j * celly,
520	<	k * cellz + 0.5 * cellz );
521	<	done = ( current_mol >= tot_nmol );
522	<	}
523	<	}
511	>	if (!done && n_per_extra > 3){
512	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
513	>	k * cellz + 0.5 * cellz);
514	>	done = (current_mol >= tot_nmol);
515	>	}
516	>	}
517		}
518		}
519		}
520
521	<	for( i=0; i<info[0].n_atoms; i++ ){
522	<	info[0].atoms[i]->setVel( vel );
521	>	for (i = 0; i < info[0].n_atoms; i++){
522	>	info[0].atoms[i]->setVel(vel);
523		}
524		}
525
526	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
526	>	void SimSetup::makeElement(double x, double y, double z){
527		int k;
528		AtomStamp* current_atom;
529		DirectionalAtom* dAtom;
530		double rotMat[3][3];
531		double pos[3];
532
533	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
534	<
535	<	current_atom = comp_stamps[current_comp]->getAtom( k );
536	<	if( !current_atom->havePosition() ){
537	<	sprintf( painCave.errMsg,
538	<	"SimSetup:initFromBass error.\n"
539	<	"\tComponent %s, atom %s does not have a position specified.\n"
540	<	"\tThe initialization routine is unable to give a start"
541	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
533	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
534	>	current_atom = comp_stamps[current_comp]->getAtom(k);
535	>	if (!current_atom->havePosition()){
536	>	sprintf(painCave.errMsg,
537	>	"SimSetup:initFromBass error.\n"
538	>	"\tComponent %s, atom %s does not have a position specified.\n"
539	>	"\tThe initialization routine is unable to give a start"
540	>	" position.\n",
541	>	comp_stamps[current_comp]->getID(), current_atom->getType());
542		painCave.isFatal = 1;
543		simError();
544		}
545	<
545	>
546		pos[0] = x + current_atom->getPosX();
547		pos[1] = y + current_atom->getPosY();
548		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
549
550	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
550	>	info[0].atoms[current_atom_ndx]->setPos(pos);
551
552	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
552	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
553	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
554
555		rotMat[0][0] = 1.0;
556		rotMat[0][1] = 0.0;
#	Line 575 | Line 564 | void SimSetup::makeElement( double x, double y, double
564		rotMat[2][1] = 0.0;
565		rotMat[2][2] = 1.0;
566
567	<	dAtom->setA( rotMat );
567	>	dAtom->setA(rotMat);
568		}
569
570		current_atom_ndx++;
#	Line 584 | Line 573 | void SimSetup::makeElement( double x, double y, double
573		current_mol++;
574		current_comp_mol++;
575
576	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
576	>	if (current_comp_mol >= components_nmol[current_comp]){
577		current_comp_mol = 0;
578		current_comp++;
579		}
580		}
581
582
583	<	void SimSetup::gatherInfo( void ){
584	<	int i,j,k;
583	>	void SimSetup::gatherInfo(void){
584	>	int i;
585
586		ensembleCase = -1;
587		ffCase = -1;
588
589		// set the easy ones first
590
591	<	for( i=0; i<nInfo; i++){
591	>	for (i = 0; i < nInfo; i++){
592		info[i].target_temp = globals->getTargetTemp();
593		info[i].dt = globals->getDt();
594		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 598 | void SimSetup::gatherInfo( void ){
598
599		// get the forceField
600
601	<	strcpy( force_field, globals->getForceField() );
601	>	strcpy(force_field, globals->getForceField());
602
603	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
604	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
605	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
603	>	if (!strcasecmp(force_field, "DUFF")){
604	>	ffCase = FF_DUFF;
605	>	}
606	>	else if (!strcasecmp(force_field, "LJ")){
607	>	ffCase = FF_LJ;
608	>	}
609	>	else if (!strcasecmp(force_field, "EAM")){
610	>	ffCase = FF_EAM;
611	>	}
612		else{
613	<	sprintf( painCave.errMsg,
614	<	"SimSetup Error. Unrecognized force field -> %s\n",
615	<	force_field );
616	<	painCave.isFatal = 1;
623	<	simError();
613	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
614	>	force_field);
615	>	painCave.isFatal = 1;
616	>	simError();
617		}
618
619	<	// get the ensemble
619	>	// get the ensemble
620
621	<	strcpy( ensemble, globals->getEnsemble() );
621	>	strcpy(ensemble, globals->getEnsemble());
622
623	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
624	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
625	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
623	>	if (!strcasecmp(ensemble, "NVE")){
624	>	ensembleCase = NVE_ENS;
625	>	}
626	>	else if (!strcasecmp(ensemble, "NVT")){
627	>	ensembleCase = NVT_ENS;
628	>	}
629	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
630		ensembleCase = NPTi_ENS;
631	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
632	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
633	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
631	>	}
632	>	else if (!strcasecmp(ensemble, "NPTf")){
633	>	ensembleCase = NPTf_ENS;
634	>	}
635	>	else if (!strcasecmp(ensemble, "NPTxyz")){
636	>	ensembleCase = NPTxyz_ENS;
637	>	}
638		else{
639	<	sprintf( painCave.errMsg,
640	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641	<	"reverting to NVE for this simulation.\n",
642	<	ensemble );
643	<	painCave.isFatal = 0;
644	<	simError();
645	<	strcpy( ensemble, "NVE" );
646	<	ensembleCase = NVE_ENS;
639	>	sprintf(painCave.errMsg,
640	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641	>	"reverting to NVE for this simulation.\n",
642	>	ensemble);
643	>	painCave.isFatal = 0;
644	>	simError();
645	>	strcpy(ensemble, "NVE");
646	>	ensembleCase = NVE_ENS;
647		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
648
649	+	for (i = 0; i < nInfo; i++){
650	+	strcpy(info[i].ensemble, ensemble);
651	+
652		// get the mixing rule
653
654	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
654	>	strcpy(info[i].mixingRule, globals->getMixingRule());
655		info[i].usePBC = globals->getPBC();
656		}
657	<
657	>
658		// get the components and calculate the tot_nMol and indvidual n_mol
659	<
659	>
660		the_components = globals->getComponents();
661		components_nmol = new int[n_components];
662
663
664	<	if( !globals->haveNMol() ){
664	>	if (!globals->haveNMol()){
665		// we don't have the total number of molecules, so we assume it is
666		// given in each component
667
668		tot_nmol = 0;
669	<	for( i=0; i<n_components; i++ ){
670	<
671	<	if( !the_components[i]->haveNMol() ){
672	<	// we have a problem
673	<	sprintf( painCave.errMsg,
674	<	"SimSetup Error. No global NMol or component NMol"
675	<	" given. Cannot calculate the number of atoms.\n" );
676	<	painCave.isFatal = 1;
677	<	simError();
669	>	for (i = 0; i < n_components; i++){
670	>	if (!the_components[i]->haveNMol()){
671	>	// we have a problem
672	>	sprintf(painCave.errMsg,
673	>	"SimSetup Error. No global NMol or component NMol"
674	>	" given. Cannot calculate the number of atoms.\n");
675	>	painCave.isFatal = 1;
676	>	simError();
677		}
678
679		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 681 | void SimSetup::gatherInfo( void ){
681		}
682		}
683		else{
684	<	sprintf( painCave.errMsg,
685	<	"SimSetup error.\n"
686	<	"\tSorry, the ability to specify total"
687	<	" nMols and then give molfractions in the components\n"
688	<	"\tis not currently supported."
689	<	" Please give nMol in the components.\n" );
684	>	sprintf(painCave.errMsg,
685	>	"SimSetup error.\n"
686	>	"\tSorry, the ability to specify total"
687	>	" nMols and then give molfractions in the components\n"
688	>	"\tis not currently supported."
689	>	" Please give nMol in the components.\n");
690		painCave.isFatal = 1;
691		simError();
692		}
693
694	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
695	+	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
696	+	sprintf(painCave.errMsg,
697	+	"Sample time is not divisible by dt \n");
698	+	painCave.isFatal = 0;
699	+	simError();
700	+	}
701	+
702	+	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
703	+	sprintf(painCave.errMsg,
704	+	"Status time is not divisible by dt\n");
705	+	painCave.isFatal = 0;
706	+	simError();
707	+	}
708	+
709	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
710	+	sprintf(painCave.errMsg,
711	+	"Thermal time is not divisible by dt\n");
712	+	painCave.isFatal = 0;
713	+	simError();
714	+	}
715	+
716	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
717	+	sprintf(painCave.errMsg,
718	+	"Reset time is not divisible by dt\n");
719	+	painCave.isFatal = 0;
720	+	simError();
721	+	}
722	+
723		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
724
725	<	if( globals->haveSampleTime() ){
725	>	for (i = 0; i < nInfo; i++){
726	>	if (globals->haveSampleTime()){
727		info[i].sampleTime = globals->getSampleTime();
728		info[i].statusTime = info[i].sampleTime;
729		info[i].thermalTime = info[i].sampleTime;
#	Line 706 | Line 733 | void SimSetup::gatherInfo( void ){
733		info[i].statusTime = info[i].sampleTime;
734		info[i].thermalTime = info[i].sampleTime;
735		}
736	<
737	<	if( globals->haveStatusTime() ){
736	>
737	>	if (globals->haveStatusTime()){
738		info[i].statusTime = globals->getStatusTime();
739		}
740	<
741	<	if( globals->haveThermalTime() ){
740	>
741	>	if (globals->haveThermalTime()){
742		info[i].thermalTime = globals->getThermalTime();
743		}
744
745	+	info[i].resetIntegrator = 0;
746	+	if( globals->haveResetTime() ){
747	+	info[i].resetTime = globals->getResetTime();
748	+	info[i].resetIntegrator = 1;
749	+	}
750	+
751		// check for the temperature set flag
752	+
753	+	if (globals->haveTempSet())
754	+	info[i].setTemp = globals->getTempSet();
755
756	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
756	>	// check for the extended State init
757	>
758	>	info[i].useInitXSstate = globals->getUseInitXSstate();
759	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
760
722	–	// get some of the tricky things that may still be in the globals
723	–
724	–	double boxVector[3];
725	–	if( globals->haveBox() ){
726	–	boxVector[0] = globals->getBox();
727	–	boxVector[1] = globals->getBox();
728	–	boxVector[2] = globals->getBox();
729	–
730	–	info[i].setBox( boxVector );
731	–	}
732	–	else if( globals->haveDensity() ){
733	–
734	–	double vol;
735	–	vol = (double)tot_nmol / globals->getDensity();
736	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	–	boxVector[1] = boxVector[0];
738	–	boxVector[2] = boxVector[0];
739	–
740	–	info[i].setBox( boxVector );
761		}
762	<	else{
763	<	if( !globals->haveBoxX() ){
764	<	sprintf( painCave.errMsg,
765	<	"SimSetup error, no periodic BoxX size given.\n" );
766	<	painCave.isFatal = 1;
767	<	simError();
762	>
763	>	//setup seed for random number generator
764	>	int seedValue;
765	>
766	>	if (globals->haveSeed()){
767	>	seedValue = globals->getSeed();
768	>
769	>	if(seedValue / 1E9 == 0){
770	>	sprintf(painCave.errMsg,
771	>	"Seed for sprng library should contain at least 9 digits\n"
772	>	"OOPSE will generate a seed for user\n");
773	>	painCave.isFatal = 0;
774	>	simError();
775	>
776	>	//using seed generated by system instead of invalid seed set by user
777	>	#ifndef IS_MPI
778	>	seedValue = make_sprng_seed();
779	>	#else
780	>	if (worldRank == 0){
781	>	seedValue = make_sprng_seed();
782		}
783	<	boxVector[0] = globals->getBoxX();
784	<
751	<	if( !globals->haveBoxY() ){
752	<	sprintf( painCave.errMsg,
753	<	"SimSetup error, no periodic BoxY size given.\n" );
754	<	painCave.isFatal = 1;
755	<	simError();
756	<	}
757	<	boxVector[1] = globals->getBoxY();
758	<
759	<	if( !globals->haveBoxZ() ){
760	<	sprintf( painCave.errMsg,
761	<	"SimSetup error, no periodic BoxZ size given.\n" );
762	<	painCave.isFatal = 1;
763	<	simError();
764	<	}
765	<	boxVector[2] = globals->getBoxZ();
766	<
767	<	info[i].setBox( boxVector );
783	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
784	>	#endif
785		}
786	+	}//end of if branch of globals->haveSeed()
787	+	else{
788	+
789	+	#ifndef IS_MPI
790	+	seedValue = make_sprng_seed();
791	+	#else
792	+	if (worldRank == 0){
793	+	seedValue = make_sprng_seed();
794	+	}
795	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
796	+	#endif
797	+	}//end of globals->haveSeed()
798
799	+	for (int i = 0; i < nInfo; i++){
800	+	info[i].setSeed(seedValue);
801		}
802	<
802	>
803		#ifdef IS_MPI
804	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
804	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
805		MPIcheckPoint();
806		#endif // is_mpi
776	–
807		}
808
809
810	<	void SimSetup::finalInfoCheck( void ){
810	>	void SimSetup::finalInfoCheck(void){
811		int index;
812		int usesDipoles;
813		int i;
814
815	<	for(i=0; i<nInfo; i++){
815	>	for (i = 0; i < nInfo; i++){
816		// check electrostatic parameters
817	<
817	>
818		index = 0;
819		usesDipoles = 0;
820	<	while( (index < info[i].n_atoms) && !usesDipoles ){
820	>	while ((index < info[i].n_atoms) && !usesDipoles){
821		usesDipoles = (info[i].atoms[index])->hasDipole();
822		index++;
823		}
824	<
824	>
825		#ifdef IS_MPI
826		int myUse = usesDipoles;
827	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
827	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828		#endif //is_mpi
829	<
829	>
830		double theEcr, theEst;
831	<
832	<	if (globals->getUseRF() ) {
831	>
832	>	if (globals->getUseRF()){
833		info[i].useReactionField = 1;
834	<
835	<	if( !globals->haveECR() ){
836	<	sprintf( painCave.errMsg,
837	<	"SimSetup Warning: using default value of 1/2 the smallest "
838	<	"box length for the electrostaticCutoffRadius.\n"
839	<	"I hope you have a very fast processor!\n");
840	<	painCave.isFatal = 0;
841	<	simError();
812	<	double smallest;
813	<	smallest = info[i].boxL[0];
814	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	<	theEcr = 0.5 * smallest;
817	<	} else {
818	<	theEcr = globals->getECR();
834	>
835	>	if (!globals->haveECR()){
836	>	sprintf(painCave.errMsg,
837	>	"SimSetup Warning: using default value of 15.0 angstroms"
838	>	"box length for the electrostaticCutoffRadius.\n");
839	>	painCave.isFatal = 0;
840	>	simError();
841	>	theEcr = 15.0;
842		}
843	<
844	<	if( !globals->haveEST() ){
822	<	sprintf( painCave.errMsg,
823	<	"SimSetup Warning: using default value of 0.05 * the "
824	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	<	);
826	<	painCave.isFatal = 0;
827	<	simError();
828	<	theEst = 0.05 * theEcr;
829	<	} else {
830	<	theEst= globals->getEST();
843	>	else{
844	>	theEcr = globals->getECR();
845		}
846	<
847	<	info[i].setEcr( theEcr, theEst );
848	<
849	<	if(!globals->haveDielectric() ){
850	<	sprintf( painCave.errMsg,
851	<	"SimSetup Error: You are trying to use Reaction Field without"
852	<	"setting a dielectric constant!\n"
853	<	);
840	<	painCave.isFatal = 1;
841	<	simError();
846	>
847	>	if (!globals->haveEST()){
848	>	sprintf(painCave.errMsg,
849	>	"SimSetup Warning: using default value of 0.05 * the "
850	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
851	>	painCave.isFatal = 0;
852	>	simError();
853	>	theEst = 0.05 * theEcr;
854		}
855	<	info[i].dielectric = globals->getDielectric();
856	<	}
845	<	else {
846	<	if (usesDipoles) {
847	<
848	<	if( !globals->haveECR() ){
849	<	sprintf( painCave.errMsg,
850	<	"SimSetup Warning: using default value of 1/2 the smallest "
851	<	"box length for the electrostaticCutoffRadius.\n"
852	<	"I hope you have a very fast processor!\n");
853	<	painCave.isFatal = 0;
854	<	simError();
855	<	double smallest;
856	<	smallest = info[i].boxL[0];
857	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	<	theEcr = 0.5 * smallest;
860	<	} else {
861	<	theEcr = globals->getECR();
862	<	}
863	<
864	<	if( !globals->haveEST() ){
865	<	sprintf( painCave.errMsg,
866	<	"SimSetup Warning: using default value of 0.05 * the "
867	<	"electrostaticCutoffRadius for the "
868	<	"electrostaticSkinThickness\n"
869	<	);
870	<	painCave.isFatal = 0;
871	<	simError();
872	<	theEst = 0.05 * theEcr;
873	<	} else {
874	<	theEst= globals->getEST();
875	<	}
876	<
877	<	info[i].setEcr( theEcr, theEst );
855	>	else{
856	>	theEst = globals->getEST();
857		}
879	–	}
880	–	}
858
859	<	#ifdef IS_MPI
883	<	strcpy( checkPointMsg, "post processing checks out" );
884	<	MPIcheckPoint();
885	<	#endif // is_mpi
859	>	info[i].setDefaultEcr(theEcr, theEst);
860
861	<	}
862	<
863	<	void SimSetup::initSystemCoords( void ){
864	<	int i;
865	<
866	<	char* inName;
867	<
868	<
869	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
870	<
871	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
861	>	if (!globals->haveDielectric()){
862	>	sprintf(painCave.errMsg,
863	>	"SimSetup Error: You are trying to use Reaction Field without"
864	>	"setting a dielectric constant!\n");
865	>	painCave.isFatal = 1;
866	>	simError();
867	>	}
868	>	info[i].dielectric = globals->getDielectric();
869	>	}
870	>	else{
871	>	if (usesDipoles){
872	>	if (!globals->haveECR()){
873	>	sprintf(painCave.errMsg,
874	>	"SimSetup Warning: using default value of 15.0 angstroms"
875	>	"box length for the electrostaticCutoffRadius.\n");
876	>	painCave.isFatal = 0;
877	>	simError();
878	>	theEcr = 15.0;
879	>	}
880	>	else{
881	>	theEcr = globals->getECR();
882	>	}
883	>
884	>	if (!globals->haveEST()){
885	>	sprintf(painCave.errMsg,
886	>	"SimSetup Warning: using default value of 0.05 * the "
887	>	"electrostaticCutoffRadius for the "
888	>	"electrostaticSkinThickness\n");
889	>	painCave.isFatal = 0;
890	>	simError();
891	>	theEst = 0.05 * theEcr;
892	>	}
893	>	else{
894	>	theEst = globals->getEST();
895	>	}
896	>
897	>	info[i].setDefaultEcr(theEcr, theEst);
898	>	}
899	>	}
900	>	}
901	>	#ifdef IS_MPI
902	>	strcpy(checkPointMsg, "post processing checks out");
903	>	MPIcheckPoint();
904	>	#endif // is_mpi
905	>	}
906
907	<	if( globals->haveInitialConfig() ){
908	<
907	>	void SimSetup::initSystemCoords(void){
908	>	int i;
909	>
910	>	char* inName;
911	>
912	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
913	>
914	>	for (i = 0; i < info[0].n_atoms; i++)
915	>	info[0].atoms[i]->setCoords();
916	>
917	>	if (globals->haveInitialConfig()){
918		InitializeFromFile* fileInit;
919		#ifdef IS_MPI // is_mpi
920	<	if( worldRank == 0 ){
920	>	if (worldRank == 0){
921		#endif //is_mpi
922		inName = globals->getInitialConfig();
923	<	fileInit = new InitializeFromFile( inName );
923	>	fileInit = new InitializeFromFile(inName);
924		#ifdef IS_MPI
925	<	}else fileInit = new InitializeFromFile( NULL );
925	>	}
926	>	else
927	>	fileInit = new InitializeFromFile(NULL);
928		#endif
929	<	fileInit->readInit( info ); // default velocities on
930	<
929	>	fileInit->readInit(info); // default velocities on
930	>
931		delete fileInit;
932		}
933		else{
934
916	–	#ifdef IS_MPI
917	–
935		// no init from bass
936
937	<	sprintf( painCave.errMsg,
938	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
939	<	painCave.isFatal;
937	>	sprintf(painCave.errMsg,
938	>	"Cannot intialize a simulation without an initial configuration file.\n");
939	>	painCave.isFatal = 1;;
940		simError();
941
925	–	#else
926	–
927	–	initFromBass();
928	–
929	–
930	–	#endif
942		}
943	<
943	>
944		#ifdef IS_MPI
945	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
945	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
946		MPIcheckPoint();
947		#endif // is_mpi
937	–
948		}
949
950
951	<	void SimSetup::makeOutNames( void ){
942	<
951	>	void SimSetup::makeOutNames(void){
952		int k;
953
945	–
946	–	for(k=0; k<nInfo; k++){
954
955	+	for (k = 0; k < nInfo; k++){
956		#ifdef IS_MPI
957	<	if( worldRank == 0 ){
957	>	if (worldRank == 0){
958		#endif // is_mpi
959	<
960	<	if( globals->haveFinalConfig() ){
961	<	strcpy( info[k].finalName, globals->getFinalConfig() );
959	>
960	>	if (globals->haveFinalConfig()){
961	>	strcpy(info[k].finalName, globals->getFinalConfig());
962		}
963		else{
964	<	strcpy( info[k].finalName, inFileName );
965	<	char* endTest;
966	<	int nameLength = strlen( info[k].finalName );
967	<	endTest = &(info[k].finalName[nameLength - 5]);
968	<	if( !strcmp( endTest, ".bass" ) ){
969	<	strcpy( endTest, ".eor" );
970	<	}
971	<	else if( !strcmp( endTest, ".BASS" ) ){
972	<	strcpy( endTest, ".eor" );
973	<	}
974	<	else{
975	<	endTest = &(info[k].finalName[nameLength - 4]);
976	<	if( !strcmp( endTest, ".bss" ) ){
977	<	strcpy( endTest, ".eor" );
978	<	}
979	<	else if( !strcmp( endTest, ".mdl" ) ){
980	<	strcpy( endTest, ".eor" );
981	<	}
982	<	else{
983	<	strcat( info[k].finalName, ".eor" );
984	<	}
985	<	}
964	>	strcpy(info[k].finalName, inFileName);
965	>	char* endTest;
966	>	int nameLength = strlen(info[k].finalName);
967	>	endTest = &(info[k].finalName[nameLength - 5]);
968	>	if (!strcmp(endTest, ".bass")){
969	>	strcpy(endTest, ".eor");
970	>	}
971	>	else if (!strcmp(endTest, ".BASS")){
972	>	strcpy(endTest, ".eor");
973	>	}
974	>	else{
975	>	endTest = &(info[k].finalName[nameLength - 4]);
976	>	if (!strcmp(endTest, ".bss")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".mdl")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	strcat(info[k].finalName, ".eor");
984	>	}
985	>	}
986		}
987	<
987	>
988		// make the sample and status out names
989	<
990	<	strcpy( info[k].sampleName, inFileName );
989	>
990	>	strcpy(info[k].sampleName, inFileName);
991		char* endTest;
992	<	int nameLength = strlen( info[k].sampleName );
992	>	int nameLength = strlen(info[k].sampleName);
993		endTest = &(info[k].sampleName[nameLength - 5]);
994	<	if( !strcmp( endTest, ".bass" ) ){
995	<	strcpy( endTest, ".dump" );
994	>	if (!strcmp(endTest, ".bass")){
995	>	strcpy(endTest, ".dump");
996		}
997	<	else if( !strcmp( endTest, ".BASS" ) ){
998	<	strcpy( endTest, ".dump" );
997	>	else if (!strcmp(endTest, ".BASS")){
998	>	strcpy(endTest, ".dump");
999		}
1000		else{
1001	<	endTest = &(info[k].sampleName[nameLength - 4]);
1002	<	if( !strcmp( endTest, ".bss" ) ){
1003	<	strcpy( endTest, ".dump" );
1004	<	}
1005	<	else if( !strcmp( endTest, ".mdl" ) ){
1006	<	strcpy( endTest, ".dump" );
1007	<	}
1008	<	else{
1009	<	strcat( info[k].sampleName, ".dump" );
1010	<	}
1001	>	endTest = &(info[k].sampleName[nameLength - 4]);
1002	>	if (!strcmp(endTest, ".bss")){
1003	>	strcpy(endTest, ".dump");
1004	>	}
1005	>	else if (!strcmp(endTest, ".mdl")){
1006	>	strcpy(endTest, ".dump");
1007	>	}
1008	>	else{
1009	>	strcat(info[k].sampleName, ".dump");
1010	>	}
1011		}
1012	<
1013	<	strcpy( info[k].statusName, inFileName );
1014	<	nameLength = strlen( info[k].statusName );
1012	>
1013	>	strcpy(info[k].statusName, inFileName);
1014	>	nameLength = strlen(info[k].statusName);
1015		endTest = &(info[k].statusName[nameLength - 5]);
1016	<	if( !strcmp( endTest, ".bass" ) ){
1017	<	strcpy( endTest, ".stat" );
1016	>	if (!strcmp(endTest, ".bass")){
1017	>	strcpy(endTest, ".stat");
1018		}
1019	<	else if( !strcmp( endTest, ".BASS" ) ){
1020	<	strcpy( endTest, ".stat" );
1019	>	else if (!strcmp(endTest, ".BASS")){
1020	>	strcpy(endTest, ".stat");
1021		}
1022		else{
1023	<	endTest = &(info[k].statusName[nameLength - 4]);
1024	<	if( !strcmp( endTest, ".bss" ) ){
1025	<	strcpy( endTest, ".stat" );
1026	<	}
1027	<	else if( !strcmp( endTest, ".mdl" ) ){
1028	<	strcpy( endTest, ".stat" );
1029	<	}
1030	<	else{
1031	<	strcat( info[k].statusName, ".stat" );
1032	<	}
1023	>	endTest = &(info[k].statusName[nameLength - 4]);
1024	>	if (!strcmp(endTest, ".bss")){
1025	>	strcpy(endTest, ".stat");
1026	>	}
1027	>	else if (!strcmp(endTest, ".mdl")){
1028	>	strcpy(endTest, ".stat");
1029	>	}
1030	>	else{
1031	>	strcat(info[k].statusName, ".stat");
1032	>	}
1033		}
1034	<
1034	>
1035		#ifdef IS_MPI
1036	+
1037		}
1038		#endif // is_mpi
1039		}
1040		}
1041
1042
1043	<	void SimSetup::sysObjectsCreation( void ){
1044	<
1045	<	int i,k;
1037	<
1043	>	void SimSetup::sysObjectsCreation(void){
1044	>	int i, k;
1045	>
1046		// create the forceField
1047
1048		createFF();
#	Line 1049 | Line 1057 | void SimSetup::sysObjectsCreation( void ){
1057
1058		#ifdef IS_MPI
1059		// divide the molecules among the processors
1060	<
1060	>
1061		mpiMolDivide();
1062		#endif //is_mpi
1063	<
1063	>
1064		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1065	<
1065	>
1066		makeSysArrays();
1067
1068		// make and initialize the molecules (all but atomic coordinates)
1069	<
1069	>
1070		makeMolecules();
1071	<
1072	<	for(k=0; k<nInfo; k++){
1071	>
1072	>	for (k = 0; k < nInfo; k++){
1073		info[k].identArray = new int[info[k].n_atoms];
1074	<	for(i=0; i<info[k].n_atoms; i++){
1074	>	for (i = 0; i < info[k].n_atoms; i++){
1075		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1076		}
1077		}
1078		}
1079
1080
1081	<	void SimSetup::createFF( void ){
1081	>	void SimSetup::createFF(void){
1082	>	switch (ffCase){
1083	>	case FF_DUFF:
1084	>	the_ff = new DUFF();
1085	>	break;
1086
1087	<	switch( ffCase ){
1087	>	case FF_LJ:
1088	>	the_ff = new LJFF();
1089	>	break;
1090
1091	<	case FF_DUFF:
1092	<	the_ff = new DUFF();
1093	<	break;
1091	>	case FF_EAM:
1092	>	the_ff = new EAM_FF();
1093	>	break;
1094
1095	<	case FF_LJ:
1096	<	the_ff = new LJFF();
1097	<	break;
1098	<
1099	<	case FF_EAM:
1086	<	the_ff = new EAM_FF();
1087	<	break;
1088	<
1089	<	default:
1090	<	sprintf( painCave.errMsg,
1091	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	<	painCave.isFatal = 1;
1093	<	simError();
1095	>	default:
1096	>	sprintf(painCave.errMsg,
1097	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1098	>	painCave.isFatal = 1;
1099	>	simError();
1100		}
1101
1102		#ifdef IS_MPI
1103	<	strcpy( checkPointMsg, "ForceField creation successful" );
1103	>	strcpy(checkPointMsg, "ForceField creation successful");
1104		MPIcheckPoint();
1105		#endif // is_mpi
1100	–
1106		}
1107
1108
1109	<	void SimSetup::compList( void ){
1105	<
1109	>	void SimSetup::compList(void){
1110		int i;
1111		char* id;
1112		LinkedMolStamp* headStamp = new LinkedMolStamp();
1113		LinkedMolStamp* currentStamp = NULL;
1114	<	comp_stamps = new MoleculeStamp*[n_components];
1115	<
1114	>	comp_stamps = new MoleculeStamp * [n_components];
1115	>
1116		// make an array of molecule stamps that match the components used.
1117		// also extract the used stamps out into a separate linked list
1118	<
1119	<	for(i=0; i<nInfo; i++){
1118	>
1119	>	for (i = 0; i < nInfo; i++){
1120		info[i].nComponents = n_components;
1121		info[i].componentsNmol = components_nmol;
1122		info[i].compStamps = comp_stamps;
1123		info[i].headStamp = headStamp;
1124		}
1121	–
1125
1123	–	for( i=0; i<n_components; i++ ){
1126
1127	+	for (i = 0; i < n_components; i++){
1128		id = the_components[i]->getType();
1129		comp_stamps[i] = NULL;
1130	<
1130	>
1131		// check to make sure the component isn't already in the list
1132
1133	<	comp_stamps[i] = headStamp->match( id );
1134	<	if( comp_stamps[i] == NULL ){
1132	<
1133	>	comp_stamps[i] = headStamp->match(id);
1134	>	if (comp_stamps[i] == NULL){
1135		// extract the component from the list;
1136	<
1137	<	currentStamp = stamps->extractMolStamp( id );
1138	<	if( currentStamp == NULL ){
1139	<	sprintf( painCave.errMsg,
1140	<	"SimSetup error: Component \"%s\" was not found in the "
1141	<	"list of declared molecules\n",
1142	<	id );
1143	<	painCave.isFatal = 1;
1144	<	simError();
1136	>
1137	>	currentStamp = stamps->extractMolStamp(id);
1138	>	if (currentStamp == NULL){
1139	>	sprintf(painCave.errMsg,
1140	>	"SimSetup error: Component \"%s\" was not found in the "
1141	>	"list of declared molecules\n",
1142	>	id);
1143	>	painCave.isFatal = 1;
1144	>	simError();
1145		}
1146	<
1147	<	headStamp->add( currentStamp );
1148	<	comp_stamps[i] = headStamp->match( id );
1146	>
1147	>	headStamp->add(currentStamp);
1148	>	comp_stamps[i] = headStamp->match(id);
1149		}
1150		}
1151
1152		#ifdef IS_MPI
1153	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1153	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1154		MPIcheckPoint();
1155		#endif // is_mpi
1156	+	}
1157
1158	+	void SimSetup::calcSysValues(void){
1159	+	int i;
1160
1161	<	}
1161	>	int* molMembershipArray;
1162
1158	–	void SimSetup::calcSysValues( void ){
1159	–	int i, j, k;
1160	–
1161	–	int *molMembershipArray;
1162	–
1163		tot_atoms = 0;
1164		tot_bonds = 0;
1165		tot_bends = 0;
1166		tot_torsions = 0;
1167	<	for( i=0; i<n_components; i++ ){
1168	<
1169	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1170	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1171	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1167	>	for (i = 0; i < n_components; i++){
1168	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1169	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1170	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1171		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1172		}
1173	<
1173	>
1174		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1175		molMembershipArray = new int[tot_atoms];
1176	<
1177	<	for(i=0; i<nInfo; i++){
1176	>
1177	>	for (i = 0; i < nInfo; i++){
1178		info[i].n_atoms = tot_atoms;
1179		info[i].n_bonds = tot_bonds;
1180		info[i].n_bends = tot_bends;
1181		info[i].n_torsions = tot_torsions;
1182		info[i].n_SRI = tot_SRI;
1183		info[i].n_mol = tot_nmol;
1184	<
1184	>
1185		info[i].molMembershipArray = molMembershipArray;
1186	<	}
1186	>	}
1187		}
1188
1189		#ifdef IS_MPI
1190
1191	<	void SimSetup::mpiMolDivide( void ){
1193	<
1191	>	void SimSetup::mpiMolDivide(void){
1192		int i, j, k;
1193		int localMol, allMol;
1194		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1195
1196	<	mpiSim = new mpiSimulation( info );
1197	<
1196	>	mpiSim = new mpiSimulation(info);
1197	>
1198		globalIndex = mpiSim->divideLabor();
1199
1200		// set up the local variables
1201	<
1201	>
1202		mol2proc = mpiSim->getMolToProcMap();
1203		molCompType = mpiSim->getMolComponentType();
1204	<
1204	>
1205		allMol = 0;
1206		localMol = 0;
1207		local_atoms = 0;
#	Line 1213 | Line 1211 | void SimSetup::mpiMolDivide( void ){
1211		globalAtomIndex = 0;
1212
1213
1214	<	for( i=0; i<n_components; i++ ){
1215	<
1216	<	for( j=0; j<components_nmol[i]; j++ ){
1217	<
1218	<	if( mol2proc[allMol] == worldRank ){
1219	<
1220	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1221	<	local_bonds +=    comp_stamps[i]->getNBonds();
1224	<	local_bends +=    comp_stamps[i]->getNBends();
1225	<	local_torsions += comp_stamps[i]->getNTorsions();
1226	<	localMol++;
1214	>	for (i = 0; i < n_components; i++){
1215	>	for (j = 0; j < components_nmol[i]; j++){
1216	>	if (mol2proc[allMol] == worldRank){
1217	>	local_atoms += comp_stamps[i]->getNAtoms();
1218	>	local_bonds += comp_stamps[i]->getNBonds();
1219	>	local_bends += comp_stamps[i]->getNBends();
1220	>	local_torsions += comp_stamps[i]->getNTorsions();
1221	>	localMol++;
1222		}
1223	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1223	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1224		info[0].molMembershipArray[globalAtomIndex] = allMol;
1225		globalAtomIndex++;
1226		}
1227
1228	<	allMol++;
1228	>	allMol++;
1229		}
1230		}
1231		local_SRI = local_bonds + local_bends + local_torsions;
1232	<
1232	>
1233		info[0].n_atoms = mpiSim->getMyNlocal();
1234	<
1235	<	if( local_atoms != info[0].n_atoms ){
1236	<	sprintf( painCave.errMsg,
1237	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	<	" localAtom (%d) are not equal.\n",
1239	<	info[0].n_atoms,
1245	<	local_atoms );
1234	>
1235	>	if (local_atoms != info[0].n_atoms){
1236	>	sprintf(painCave.errMsg,
1237	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	>	" localAtom (%d) are not equal.\n",
1239	>	info[0].n_atoms, local_atoms);
1240		painCave.isFatal = 1;
1241		simError();
1242		}
#	Line 1253 | Line 1247 | void SimSetup::mpiMolDivide( void ){
1247		info[0].n_SRI = local_SRI;
1248		info[0].n_mol = localMol;
1249
1250	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1250	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1251		MPIcheckPoint();
1252		}
1253	<
1253	>
1254		#endif // is_mpi
1255
1256
1257	<	void SimSetup::makeSysArrays( void ){
1258	<	int i, j, k, l;
1257	>	void SimSetup::makeSysArrays(void){
1258	>
1259	>	#ifndef IS_MPI
1260	>	int k, j;
1261	>	#endif // is_mpi
1262	>	int i, l;
1263
1264		Atom** the_atoms;
1265		Molecule* the_molecules;
1266		Exclude** the_excludes;
1267
1268	<
1269	<	for(l=0; l<nInfo; l++){
1272	<
1268	>
1269	>	for (l = 0; l < nInfo; l++){
1270		// create the atom and short range interaction arrays
1271	<
1272	<	the_atoms = new Atom*[info[l].n_atoms];
1271	>
1272	>	the_atoms = new Atom * [info[l].n_atoms];
1273		the_molecules = new Molecule[info[l].n_mol];
1274		int molIndex;
1275
1276		// initialize the molecule's stampID's
1277	<
1277	>
1278		#ifdef IS_MPI
1279	<
1280	<
1279	>
1280	>
1281		molIndex = 0;
1282	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1283	<
1284	<	if(mol2proc[i] == worldRank ){
1285	<	the_molecules[molIndex].setStampID( molCompType[i] );
1286	<	the_molecules[molIndex].setMyIndex( molIndex );
1287	<	the_molecules[molIndex].setGlobalIndex( i );
1291	<	molIndex++;
1282	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1283	>	if (mol2proc[i] == worldRank){
1284	>	the_molecules[molIndex].setStampID(molCompType[i]);
1285	>	the_molecules[molIndex].setMyIndex(molIndex);
1286	>	the_molecules[molIndex].setGlobalIndex(i);
1287	>	molIndex++;
1288		}
1289		}
1290	<
1290	>
1291		#else // is_mpi
1292	<
1292	>
1293		molIndex = 0;
1294		globalAtomIndex = 0;
1295	<	for(i=0; i<n_components; i++){
1296	<	for(j=0; j<components_nmol[i]; j++ ){
1297	<	the_molecules[molIndex].setStampID( i );
1298	<	the_molecules[molIndex].setMyIndex( molIndex );
1299	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1300	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1301	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	<	globalAtomIndex++;
1303	<	}
1304	<	molIndex++;
1295	>	for (i = 0; i < n_components; i++){
1296	>	for (j = 0; j < components_nmol[i]; j++){
1297	>	the_molecules[molIndex].setStampID(i);
1298	>	the_molecules[molIndex].setMyIndex(molIndex);
1299	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1300	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1301	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	>	globalAtomIndex++;
1303	>	}
1304	>	molIndex++;
1305		}
1306		}
1307	<
1308	<
1307	>
1308	>
1309		#endif // is_mpi
1310
1311
1312	<	if( info[l].n_SRI ){
1317	<
1312	>	if (info[l].n_SRI){
1313		Exclude::createArray(info[l].n_SRI);
1314	<	the_excludes = new Exclude*[info[l].n_SRI];
1315	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1316	<	the_excludes[ex] = new Exclude(ex);
1314	>	the_excludes = new Exclude * [info[l].n_SRI];
1315	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	>	the_excludes[ex] = new Exclude(ex);
1317		}
1318		info[l].globalExcludes = new int;
1319		info[l].n_exclude = info[l].n_SRI;
1320		}
1321		else{
1322	<
1323	<	Exclude::createArray( 1 );
1329	<	the_excludes = new Exclude*;
1322	>	Exclude::createArray(1);
1323	>	the_excludes = new Exclude * ;
1324		the_excludes[0] = new Exclude(0);
1325	<	the_excludes[0]->setPair( 0,0 );
1325	>	the_excludes[0]->setPair(0, 0);
1326		info[l].globalExcludes = new int;
1327		info[l].globalExcludes[0] = 0;
1328		info[l].n_exclude = 0;
#	Line 1341 | Line 1335 | void SimSetup::makeSysArrays( void ){
1335		info[l].nGlobalExcludes = 0;
1336		info[l].excludes = the_excludes;
1337
1338	<	the_ff->setSimInfo( info );
1345	<
1338	>	the_ff->setSimInfo(info);
1339		}
1340		}
1341
1342	<	void SimSetup::makeIntegrator( void ){
1350	<
1342	>	void SimSetup::makeIntegrator(void){
1343		int k;
1344
1345	<	NVT<RealIntegrator>*  myNVT = NULL;
1346	<	NPTi<RealIntegrator>* myNPTi = NULL;
1347	<	NPTf<RealIntegrator>* myNPTf = NULL;
1348	<	NPTim<RealIntegrator>* myNPTim = NULL;
1349	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1350	<
1351	<	for(k=0; k<nInfo; k++){
1352	<
1353	<	switch( ensembleCase ){
1354	<
1355	<	case NVE_ENS:
1356	<	if (globals->haveZconstraints()){
1357	<	setupZConstraint(info[k]);
1358	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1345	>	NVE<RealIntegrator>* myNVE = NULL;
1346	>	NVT<RealIntegrator>* myNVT = NULL;
1347	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1349	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1350	>
1351	>	for (k = 0; k < nInfo; k++){
1352	>	switch (ensembleCase){
1353	>	case NVE_ENS:
1354	>	if (globals->haveZconstraints()){
1355	>	setupZConstraint(info[k]);
1356	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1357	>	}
1358	>	else{
1359	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1360		}
1361	<
1362	<	else
1363	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1371	<	break;
1372	<
1373	<	case NVT_ENS:
1374	<	if (globals->haveZconstraints()){
1375	<	setupZConstraint(info[k]);
1376	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377	<	}
1378	<	else
1379	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1361	>
1362	>	info->the_integrator = myNVE;
1363	>	break;
1364
1365	<	myNVT->setTargetTemp(globals->getTargetTemp());
1366	<
1367	<	if (globals->haveTauThermostat())
1368	<	myNVT->setTauThermostat(globals->getTauThermostat());
1369	<
1370	<	else {
1371	<	sprintf( painCave.errMsg,
1388	<	"SimSetup error: If you use the NVT\n"
1389	<	"    ensemble, you must set tauThermostat.\n");
1390	<	painCave.isFatal = 1;
1391	<	simError();
1392	<	}
1393	<	break;
1394	<
1395	<	case NPTi_ENS:
1396	<	if (globals->haveZconstraints()){
1397	<	setupZConstraint(info[k]);
1398	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399	<	}
1400	<	else
1401	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1365	>	case NVT_ENS:
1366	>	if (globals->haveZconstraints()){
1367	>	setupZConstraint(info[k]);
1368	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1369	>	}
1370	>	else
1371	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1372
1373	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1404	<
1405	<	if (globals->haveTargetPressure())
1406	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	<	else {
1408	<	sprintf( painCave.errMsg,
1409	<	"SimSetup error: If you use a constant pressure\n"
1410	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	<	painCave.isFatal = 1;
1412	<	simError();
1413	<	}
1414	<
1415	<	if( globals->haveTauThermostat() )
1416	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	<	else{
1418	<	sprintf( painCave.errMsg,
1419	<	"SimSetup error: If you use an NPT\n"
1420	<	"    ensemble, you must set tauThermostat.\n");
1421	<	painCave.isFatal = 1;
1422	<	simError();
1423	<	}
1424	<
1425	<	if( globals->haveTauBarostat() )
1426	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	<	else{
1428	<	sprintf( painCave.errMsg,
1429	<	"SimSetup error: If you use an NPT\n"
1430	<	"    ensemble, you must set tauBarostat.\n");
1431	<	painCave.isFatal = 1;
1432	<	simError();
1433	<	}
1434	<	break;
1435	<
1436	<	case NPTf_ENS:
1437	<	if (globals->haveZconstraints()){
1438	<	setupZConstraint(info[k]);
1439	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440	<	}
1441	<	else
1442	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1373	>	myNVT->setTargetTemp(globals->getTargetTemp());
1374
1375	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1376	<
1377	<	if (globals->haveTargetPressure())
1378	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1379	<	else {
1380	<	sprintf( painCave.errMsg,
1381	<	"SimSetup error: If you use a constant pressure\n"
1382	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1383	<	painCave.isFatal = 1;
1453	<	simError();
1454	<	}
1455	<
1456	<	if( globals->haveTauThermostat() )
1457	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1458	<	else{
1459	<	sprintf( painCave.errMsg,
1460	<	"SimSetup error: If you use an NPT\n"
1461	<	"    ensemble, you must set tauThermostat.\n");
1462	<	painCave.isFatal = 1;
1463	<	simError();
1464	<	}
1465	<
1466	<	if( globals->haveTauBarostat() )
1467	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1468	<	else{
1469	<	sprintf( painCave.errMsg,
1470	<	"SimSetup error: If you use an NPT\n"
1471	<	"    ensemble, you must set tauBarostat.\n");
1472	<	painCave.isFatal = 1;
1473	<	simError();
1474	<	}
1475	<	break;
1476	<
1477	<	case NPTim_ENS:
1478	<	if (globals->haveZconstraints()){
1479	<	setupZConstraint(info[k]);
1480	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481	<	}
1482	<	else
1483	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1375	>	if (globals->haveTauThermostat())
1376	>	myNVT->setTauThermostat(globals->getTauThermostat());
1377	>	else{
1378	>	sprintf(painCave.errMsg,
1379	>	"SimSetup error: If you use the NVT\n"
1380	>	"    ensemble, you must set tauThermostat.\n");
1381	>	painCave.isFatal = 1;
1382	>	simError();
1383	>	}
1384
1385	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1386	<
1487	<	if (globals->haveTargetPressure())
1488	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1489	<	else {
1490	<	sprintf( painCave.errMsg,
1491	<	"SimSetup error: If you use a constant pressure\n"
1492	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1493	<	painCave.isFatal = 1;
1494	<	simError();
1495	<	}
1496	<
1497	<	if( globals->haveTauThermostat() )
1498	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1499	<	else{
1500	<	sprintf( painCave.errMsg,
1501	<	"SimSetup error: If you use an NPT\n"
1502	<	"    ensemble, you must set tauThermostat.\n");
1503	<	painCave.isFatal = 1;
1504	<	simError();
1505	<	}
1506	<
1507	<	if( globals->haveTauBarostat() )
1508	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509	<	else{
1510	<	sprintf( painCave.errMsg,
1511	<	"SimSetup error: If you use an NPT\n"
1512	<	"    ensemble, you must set tauBarostat.\n");
1513	<	painCave.isFatal = 1;
1514	<	simError();
1515	<	}
1516	<	break;
1517	<
1518	<	case NPTfm_ENS:
1519	<	if (globals->haveZconstraints()){
1520	<	setupZConstraint(info[k]);
1521	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522	<	}
1523	<	else
1524	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1385	>	info->the_integrator = myNVT;
1386	>	break;
1387
1388	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1389	<
1390	<	if (globals->haveTargetPressure())
1391	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1392	<	else {
1393	<	sprintf( painCave.errMsg,
1394	<	"SimSetup error: If you use a constant pressure\n"
1395	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1396	<	painCave.isFatal = 1;
1397	<	simError();
1398	<	}
1399	<
1400	<	if( globals->haveTauThermostat() )
1401	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1402	<	else{
1403	<	sprintf( painCave.errMsg,
1404	<	"SimSetup error: If you use an NPT\n"
1405	<	"    ensemble, you must set tauThermostat.\n");
1406	<	painCave.isFatal = 1;
1407	<	simError();
1408	<	}
1409	<
1410	<	if( globals->haveTauBarostat() )
1411	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1412	<	else{
1413	<	sprintf( painCave.errMsg,
1414	<	"SimSetup error: If you use an NPT\n"
1415	<	"    ensemble, you must set tauBarostat.\n");
1416	<	painCave.isFatal = 1;
1417	<	simError();
1418	<	}
1419	<	break;
1420	<
1421	<	default:
1422	<	sprintf( painCave.errMsg,
1423	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1424	<	painCave.isFatal = 1;
1425	<	simError();
1388	>	case NPTi_ENS:
1389	>	if (globals->haveZconstraints()){
1390	>	setupZConstraint(info[k]);
1391	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1392	>	}
1393	>	else
1394	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1395	>
1396	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1397	>
1398	>	if (globals->haveTargetPressure())
1399	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1400	>	else{
1401	>	sprintf(painCave.errMsg,
1402	>	"SimSetup error: If you use a constant pressure\n"
1403	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1404	>	painCave.isFatal = 1;
1405	>	simError();
1406	>	}
1407	>
1408	>	if (globals->haveTauThermostat())
1409	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1410	>	else{
1411	>	sprintf(painCave.errMsg,
1412	>	"SimSetup error: If you use an NPT\n"
1413	>	"    ensemble, you must set tauThermostat.\n");
1414	>	painCave.isFatal = 1;
1415	>	simError();
1416	>	}
1417	>
1418	>	if (globals->haveTauBarostat())
1419	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1420	>	else{
1421	>	sprintf(painCave.errMsg,
1422	>	"SimSetup error: If you use an NPT\n"
1423	>	"    ensemble, you must set tauBarostat.\n");
1424	>	painCave.isFatal = 1;
1425	>	simError();
1426	>	}
1427	>
1428	>	info->the_integrator = myNPTi;
1429	>	break;
1430	>
1431	>	case NPTf_ENS:
1432	>	if (globals->haveZconstraints()){
1433	>	setupZConstraint(info[k]);
1434	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1435	>	}
1436	>	else
1437	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1438	>
1439	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1440	>
1441	>	if (globals->haveTargetPressure())
1442	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1443	>	else{
1444	>	sprintf(painCave.errMsg,
1445	>	"SimSetup error: If you use a constant pressure\n"
1446	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1447	>	painCave.isFatal = 1;
1448	>	simError();
1449	>	}
1450	>
1451	>	if (globals->haveTauThermostat())
1452	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1453	>
1454	>	else{
1455	>	sprintf(painCave.errMsg,
1456	>	"SimSetup error: If you use an NPT\n"
1457	>	"    ensemble, you must set tauThermostat.\n");
1458	>	painCave.isFatal = 1;
1459	>	simError();
1460	>	}
1461	>
1462	>	if (globals->haveTauBarostat())
1463	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1464	>
1465	>	else{
1466	>	sprintf(painCave.errMsg,
1467	>	"SimSetup error: If you use an NPT\n"
1468	>	"    ensemble, you must set tauBarostat.\n");
1469	>	painCave.isFatal = 1;
1470	>	simError();
1471	>	}
1472	>
1473	>	info->the_integrator = myNPTf;
1474	>	break;
1475	>
1476	>	case NPTxyz_ENS:
1477	>	if (globals->haveZconstraints()){
1478	>	setupZConstraint(info[k]);
1479	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1480	>	}
1481	>	else
1482	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1483	>
1484	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1485	>
1486	>	if (globals->haveTargetPressure())
1487	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1488	>	else{
1489	>	sprintf(painCave.errMsg,
1490	>	"SimSetup error: If you use a constant pressure\n"
1491	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1492	>	painCave.isFatal = 1;
1493	>	simError();
1494	>	}
1495	>
1496	>	if (globals->haveTauThermostat())
1497	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1498	>	else{
1499	>	sprintf(painCave.errMsg,
1500	>	"SimSetup error: If you use an NPT\n"
1501	>	"    ensemble, you must set tauThermostat.\n");
1502	>	painCave.isFatal = 1;
1503	>	simError();
1504	>	}
1505	>
1506	>	if (globals->haveTauBarostat())
1507	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1508	>	else{
1509	>	sprintf(painCave.errMsg,
1510	>	"SimSetup error: If you use an NPT\n"
1511	>	"    ensemble, you must set tauBarostat.\n");
1512	>	painCave.isFatal = 1;
1513	>	simError();
1514	>	}
1515	>
1516	>	info->the_integrator = myNPTxyz;
1517	>	break;
1518	>
1519	>	default:
1520	>	sprintf(painCave.errMsg,
1521	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1522	>	painCave.isFatal = 1;
1523	>	simError();
1524		}
1525		}
1526		}
1527
1528	<	void SimSetup::initFortran( void ){
1569	<
1528	>	void SimSetup::initFortran(void){
1529		info[0].refreshSim();
1530	<
1531	<	if( !strcmp( info[0].mixingRule, "standard") ){
1532	<	the_ff->initForceField( LB_MIXING_RULE );
1530	>
1531	>	if (!strcmp(info[0].mixingRule, "standard")){
1532	>	the_ff->initForceField(LB_MIXING_RULE);
1533		}
1534	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1535	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1534	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1535	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1536		}
1537		else{
1538	<	sprintf( painCave.errMsg,
1539	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	<	info[0].mixingRule );
1538	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1539	>	info[0].mixingRule);
1540		painCave.isFatal = 1;
1541		simError();
1542		}
1543
1544
1545		#ifdef IS_MPI
1546	<	strcpy( checkPointMsg,
1589	<	"Successfully intialized the mixingRule for Fortran." );
1546	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1547		MPIcheckPoint();
1548		#endif // is_mpi
1592	–
1549		}
1550
1551	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1552	<	{
1553	<	int nZConstraints;
1598	<	ZconStamp** zconStamp;
1599	<
1600	<	if(globals->haveZconstraintTime()){
1601	<
1602	<	//add sample time of z-constraint  into SimInfo's property list
1603	<	DoubleData* zconsTimeProp = new DoubleData();
1604	<	zconsTimeProp->setID(ZCONSTIME_ID);
1605	<	zconsTimeProp->setData(globals->getZconsTime());
1606	<	theInfo.addProperty(zconsTimeProp);
1607	<	}
1608	<	else{
1609	<	sprintf( painCave.errMsg,
1610	<	"ZConstraint error: If you use an ZConstraint\n"
1611	<	" , you must set sample time.\n");
1612	<	painCave.isFatal = 1;
1613	<	simError();
1614	<	}
1551	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1552	>	int nZConstraints;
1553	>	ZconStamp** zconStamp;
1554
1555	<	//
1556	<	nZConstraints = globals->getNzConstraints();
1557	<	zconStamp = globals->getZconStamp();
1558	<	ZConsParaItem tempParaItem;
1555	>	if (globals->haveZconstraintTime()){
1556	>	//add sample time of z-constraint  into SimInfo's property list
1557	>	DoubleData* zconsTimeProp = new DoubleData();
1558	>	zconsTimeProp->setID(ZCONSTIME_ID);
1559	>	zconsTimeProp->setData(globals->getZconsTime());
1560	>	theInfo.addProperty(zconsTimeProp);
1561	>	}
1562	>	else{
1563	>	sprintf(painCave.errMsg,
1564	>	"ZConstraint error: If you use an ZConstraint\n"
1565	>	" , you must set sample time.\n");
1566	>	painCave.isFatal = 1;
1567	>	simError();
1568	>	}
1569
1570	<	ZConsParaData* zconsParaData = new ZConsParaData();
1571	<	zconsParaData->setID(ZCONSPARADATA_ID);
1572	<
1573	<	for(int i = 0; i < nZConstraints; i++){
1570	>	//push zconsTol into siminfo, if user does not specify
1571	>	//value for zconsTol, a default value will be used
1572	>	DoubleData* zconsTol = new DoubleData();
1573	>	zconsTol->setID(ZCONSTOL_ID);
1574	>	if (globals->haveZconsTol()){
1575	>	zconsTol->setData(globals->getZconsTol());
1576	>	}
1577	>	else{
1578	>	double defaultZConsTol = 0.01;
1579	>	sprintf(painCave.errMsg,
1580	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1581	>	" , default value %f is used.\n",
1582	>	defaultZConsTol);
1583	>	painCave.isFatal = 0;
1584	>	simError();
1585	>
1586	>	zconsTol->setData(defaultZConsTol);
1587	>	}
1588	>	theInfo.addProperty(zconsTol);
1589	>
1590	>	//set Force Subtraction Policy
1591	>	StringData* zconsForcePolicy = new StringData();
1592	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1593	>
1594	>	if (globals->haveZconsForcePolicy()){
1595	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1596	>	}
1597	>	else{
1598	>	sprintf(painCave.errMsg,
1599	>	"ZConstraint Warning: User does not set force Subtraction policy, "
1600	>	"PolicyByMass is used\n");
1601	>	painCave.isFatal = 0;
1602	>	simError();
1603	>	zconsForcePolicy->setData("BYMASS");
1604	>	}
1605	>
1606	>	theInfo.addProperty(zconsForcePolicy);
1607	>
1608	>	//Determine the name of ouput file and add it into SimInfo's property list
1609	>	//Be careful, do not use inFileName, since it is a pointer which
1610	>	//point to a string at master node, and slave nodes do not contain that string
1611	>
1612	>	string zconsOutput(theInfo.finalName);
1613	>
1614	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1615	>
1616	>	StringData* zconsFilename = new StringData();
1617	>	zconsFilename->setID(ZCONSFILENAME_ID);
1618	>	zconsFilename->setData(zconsOutput);
1619	>
1620	>	theInfo.addProperty(zconsFilename);
1621	>
1622	>	//setup index, pos and other parameters of z-constraint molecules
1623	>	nZConstraints = globals->getNzConstraints();
1624	>	theInfo.nZconstraints = nZConstraints;
1625	>
1626	>	zconStamp = globals->getZconStamp();
1627	>	ZConsParaItem tempParaItem;
1628	>
1629	>	ZConsParaData* zconsParaData = new ZConsParaData();
1630	>	zconsParaData->setID(ZCONSPARADATA_ID);
1631	>
1632	>	for (int i = 0; i < nZConstraints; i++){
1633		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1634		tempParaItem.zPos = zconStamp[i]->getZpos();
1635		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1636		tempParaItem.kRatio = zconStamp[i]->getKratio();
1637
1638		zconsParaData->addItem(tempParaItem);
1639	<	}
1639	>	}
1640
1641	<	//sort the parameters by index of molecules
1642	<	zconsParaData->sortByIndex();
1643	<
1644	<	//push data into siminfo, therefore, we can retrieve later
1645	<	theInfo.addProperty(zconsParaData);
1641	>	//check the uniqueness of index
1642	>	if(!zconsParaData->isIndexUnique()){
1643	>	sprintf(painCave.errMsg,
1644	>	"ZConstraint Error: molIndex is not unique\n");
1645	>	painCave.isFatal = 1;
1646	>	simError();
1647	>	}
1648
1649	<	//push zconsTol into siminfo, if user does not specify
1650	<	//value for zconsTol, a default value will be used
1651	<	DoubleData* zconsTol = new DoubleData();
1652	<	zconsTol->setID(ZCONSTOL_ID);
1653	<	if(globals->haveZconsTol()){
1644	<	zconsTol->setData(globals->getZconsTol());
1645	<	}
1646	<	else{
1647	<	double defaultZConsTol = 1E-6;
1648	<	sprintf( painCave.errMsg,
1649	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1650	<	" , default value %f is used.\n", defaultZConsTol);
1651	<	painCave.isFatal = 0;
1652	<	simError();
1653	<
1654	<	zconsTol->setData(defaultZConsTol);
1655	<	}
1656	<	theInfo.addProperty(zconsTol);
1657	<
1658	<	//Determine the name of ouput file and add it into SimInfo's property list
1659	<	//Be careful, do not use inFileName, since it is a pointer which
1660	<	//point to a string at master node, and slave nodes do not contain that string
1661	<
1662	<	string zconsOutput(theInfo.finalName);
1663	<
1664	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1665	<
1666	<	StringData* zconsFilename = new StringData();
1667	<	zconsFilename->setID(ZCONSFILENAME_ID);
1668	<	zconsFilename->setData(zconsOutput);
1669	<
1670	<	theInfo.addProperty(zconsFilename);
1649	>	//sort the parameters by index of molecules
1650	>	zconsParaData->sortByIndex();
1651	>
1652	>	//push data into siminfo, therefore, we can retrieve later
1653	>	theInfo.addProperty(zconsParaData);
1654		}

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